We observed temperature variations over 10 months within a Kuroko ore (hydrothermal sulfide) cultivation apparatus installed atop a 50-m-deep borehole drilled in the Noho hydrothermal system in the mid-Okinawa Trough, southwestern Japan, for monitoring of hydrothermal fluids and in situ mineral precipitation experiments. Temperature and pressure in the apparatus fluctuated with the tidal period immediately after its installation. Initially, the average temperature was 75–76 °C and the amplitude of the semi-diurnal tidal temperature modulation was ~0.3 °C. Four months later, the amplitude of tidal temperature modulation had gradually increased to 4 °C in synchrony with an average temperature decrease to ~40 °C. Numerical modeling showed that both the increase in tidal amplitude and the decrease in average temperature were attributable to a gradual decrease in inflow to the apparatus, which promoted conductive cooling through the pipe wall. The reduced inflow was probably caused by clogging inside the apparatus, but we cannot rule out a natural cause, because the drilling would have significantly decreased the volume of hot fluid in the reservoir. The temperature fluctuation phase lagged the pressure fluctuation phase by ~150°. Assuming that the fluctuations originated from inflow from the reservoir, we conducted 2-D numerical hydrothermal modeling for a poroelastic medium. To generate the 150° phase lag, the permeability in the reservoir needed to exceed that in the ambient formation by ~3 orders of magnitude. The tidal variation phase can be a useful tool for assessing the hydrological state and response of a hydrothermal system.